1 / 14

Python-based Tools and Web Services for Structural Bioinformatics

Python-based Tools and Web Services for Structural Bioinformatics. Randy Heiland, Charles Moad IU Pervasive Technology Labs Sean Mooney, IU School of Medicine {heiland,cmoad}@indiana.edu sdmooney@iupui.edu. Outline. Past Python-related work (at NCSA, no proteomics)

webster
Télécharger la présentation

Python-based Tools and Web Services for Structural Bioinformatics

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Python-based Tools and Web Services for Structural Bioinformatics Randy Heiland, Charles Moad IU Pervasive Technology Labs Sean Mooney, IU School of Medicine {heiland,cmoad}@indiana.edu sdmooney@iupui.edu

  2. Outline • Past Python-related work (at NCSA, no proteomics) • Indiana University/IUPUI: Pervasive Tech Labs, Center for Computational Biology and Bioinformatics • Intro to Structural Bioinformatics • Tools/Services for Mutation Data • Vis tools (UCSF Chimera, PyMOL) • Web Services (Axis, Pywebsvcs/SOAPpy) • Future work

  3. Past Python-related work • Python-wrapped VTK [+ pyMPI] for [cluster-based] SciVis • VisBench project: client-server vis & analysis (RH at UIUC/NCSA ’97-’03) Java Swing client CORBA/XML-RPC Python-VTK server Jython Access Grid™ (AG2)

  4. Indiana University; IUPUI • Pervasive Technology Labs at IU – six labs pervasive.iu.edu (~1999), sda.iu.edu (2003) • Help grow the IT economy in Indiana via collaborations in academia and industry • Center for Computational Biology and Bioinformatics - Mooney Lab compbio.iupui.edu/mooney (2003) • Characterize the structural elements that enable protein function • Understand the effects of genomic variation on the proteome

  5. Some terminology • Cell contains genome = complete set of DNA • DNA = sequence of ATCG nucleotides • Genes = specific seqs that encode instructions for making proteins • Protein = molecules of (20) amino acids that perform much of life’s function • Proteome = set of all proteins in a cell • Proteomics = study of protein’s structure & function • Bioinformatics = Biology + CS + IT

  6. Intro to Structural Bioinformatics • Protein Data Bank now contains more than 26,000 structures • Annotation of structural data is a challenging and relevant problem

  7. Protein visualization tools • UCSF Chimera (www.cgl.ucsf.edu/chimera) • PyMOL (pymol.sourceforge.net) • Python-based tools for interactive visualization of protein 3-D structure (& 1-D sequence) • Each provides a Python-based API for writing extensions

  8. Web Services • Any service that is: • available over the Internet • uses XML messaging • independent of OS & pgming lng • XML messaging: • XML-RPC, SOAP, HTTP post/get • WSDL: Web Svcs Description Lng For MutDB: • Apache Axis (ws.apache.org/axis) • PyWebSvcs/SOAPpy (pywebsvcs.sf.net)

  9. Examples of Bio Web Services • New PDB (pdbbeta.rcsb.org/pdb) • alpha.rcsb.org/jboss-net/services/pdbWebService?wsdl • KEGG (www.genome.jp/kegg/soap) • biomoby.org • Google ‘bio web services’

  10. MutDB (http://www.mutdb.org) MutDB provides structural annotations for disease-associated mutations and single nucleotide polymorphisms (SNPs)

  11. Structural Mutation Service • Mutations on MutDB are mapped to protein structure • Extension in Chimera queries MutDB UCSF Chimera extension

  12. PyMol Extension Controller window identifies mapped mutation positions which are highlighted structurally

  13. Future work • Web services for identifying regions of structural similarity between a query protein and a database of protein structures Chimera PyMOL matplotlib

  14. Acknowledgements & Ref The Indiana Genomics Initiative (INGEN) and the Pervasive Technology Labs of Indiana University are supported in part by Lilly Endowment Inc. S.D. Mooney and R.B. Altman, “MutDB: annotating human variation with functionally relevant data”. Bioinformatics. 2003 Sep 22;19(14):1858-1860

More Related